•Using landscape ecology on ES is appropriate to better understand urbanization dynamics in Latin America.•Patterns of ES in Latin America differ as a consequence of climate and green governance.•Urban vegetation cover is not the only factor influencing urban ecosystem services, also important is its structure, composition and fragmentation.•Fragmentation of ES can inform decision-making for reducing environmental inequalities. Latin America is one of the most urbanized region in the world, where patterns of urbanization are disorganized and disjoint from urban planning, with unknown effects for ecosystem services (ES). We evaluated the ES in Bogota and Santiago for a 30-year period. Using remote sensing data, models and census data we quantified carbon regulation, climate mitigation and recreation potential. We assessed ES provision changes and their spatio-temporal patterns using landscape metrics. Urban vegetation patterns differ between the two cities because of climate variability and greening policies. Bogota stored more carbon than Santiago given to climate effects, differences within city were the result of different policies and management. Climate mitigation showed similar behavior for both cities, influenced by global climate, densification and urban sprawling. Recreation potential increased in the inner-city and decrease at the outskirts, reflecting unplanned urban sprawling and increase population. Areas of high ecosystem services connected for Bogota and fragmented for Santiago. Bogota improved its environmental condition, as evaluated by ES provision, while Santiago worsens, even there was an increased in vegetation cover. Vegetation cover was not a sufficient indicator for ecosystem services and the distribution of it becomes highly relevant for informing mismatches between services and vegetation.